Pre-modern humans may have picked up genes from Homo erectus

Denisova cave serves up a new genome, this time Neanderthal.

Excavations in the Denisovan cave have yielded tiny bone fragments that have had an outsized impact on our understanding of human evolution.

Bence Viola

It's a busy time in our attempts to study our species' pre-modern history. Just two weeks ago, researchers reported the sequence of the oldest bones to yield human DNA. Now, the same research group is back with an entire genome, obtained from a bone found in Siberia's Denisova cave. This genome comes from a Neanderthal, but all the data reveals a lot about all the interconnections among the pre-modern human groups that were wandering around Eurasia tens of thousands of years ago. The analysis came with a tantalizing hint that one of those groups had interbred with a species separated from modern humans by over a million years—perhaps Homo erectus.

The Denisova cave is famous for having yielded the bones that helped us identify the Denisovans, a group of archaic humans that inhabited Asia at the same time as the Neanderthals. Although we haven't found enough bones to know much about what the Denisovans looked like, DNA analysis has revealed that they are most closely related to Neanderthals and that they interbred with modern humans that went on to populate East Asia, the Americas, and the Pacific.

The new results spring from a toe bone found in the same cave, this one from a layer that is estimated to be tens of thousands of years earlier. DNA sequencing revealed the bone to be from a Neanderthal, a different group of pre-modern humans that is most closely related to the Denisovans. The DNA was in excellent condition and had a minimal (about one percent) contamination with sequences from modern humans. The team generated a high-quality genome using samples from this bone.

The sequence that resulted tells us a lot about Neanderthals. For one, it shows that other populations we've obtained DNA from (samples found in the Caucasus and Croatia) were closely related but distinct, indicating that the Neanderthals were already well established by the time this individual died. Those populations were apparently quite small, however, since there's not a lot of genetic diversity among them. In the case of the specific individual in the Denisovan cave, the lack of diversity was quite severe. Rather than carrying two distinct sets of chromosomes, large stretches of the two chromosomes were identical, indicating that they were inherited from a single individual in the recent past.

The extent of this identity suggests that the parents of this individual were half-siblings, although other combinations (uncle-niece, aunt-nephew) would also produce a similar pattern.

But the more significant results come from what this new sequence tells us about the other groups of humans present at the time, including modern humans. To begin with, it confirms the rough timing of the split between the ancestors of modern humans and the ancestors of Neanderthals and Denisovans, which took place about 550,000-600,000 years ago. The Neanderthals and Denisovans became a distinct population about 400,000 years ago.

The sequence also provides a clearer estimate of the amount of Neanderthal DNA that shows up in modern human populations: 1.5 to 2.1 percent. And it confirms that it got there via interbreeding, since the Neanderthal sequence looks most similar to the sample obtained from the Caucasus remains. Had it been inherited through a structured ancestral population in Africa, it should look like it was equally distant from all three of the Neanderthal genomes. The other thing that's apparent is that modern Asian and American populations have a bit more Neanderthal DNA than others, suggesting that a low amount of interbreeding continued as our ancestors moved east.

Our ancestors weren't the only ones who couldn't resist getting a piece of the Neanderthals. At least a half percent of the Denisovan genome also came from them as well.

But perhaps the most unexpected finding comes from a comparison with the Denisovan genome. Modern humans in Africa never overlapped geographically with Neanderthals or Denisovans and thus contain none of their DNA. Therefore, any shared DNA they have should be inherited from a common ancestor, and the African's should be equally distant from the Neanderthals and Denisovans. Yet they're not. The Denisovans have some sequences that are much more distant than you'd expect.

After considering and rejecting a couple of alternative explanations for this, the paper settles on a rather radical explanation: Denisovans themselves interbred with a population that had been separated from their common ancestor with modern humans for about a million years. This, as the authors note, suggests that the DNA's source was Homo erectus. In fact, they suggest that the Denisovan's entire mitochondrial genome might have come from this interbreeding event, since it's much more distant from the Neanderthals' than the rest of the genome is.

Of course, that explanation is even harder to square with the findings from the ancient bones in Spain, which had a similar sequence but came from skeletons that looked somewhat like Neanderthals. Unless, of course, the Spanish population also interbred with Homo erectus (or whatever this is) at some point.

In any case, the results add yet another layer onto the increasingly complicated Out-of-Africa model of the origin of modern humans. We still arose in Africa and migrated out into Eurasia. But once we got there, we interbred with a previous wave of African expatriates and incorporated a small bit of their genetic legacy into our own. And one part of that previous wave may have even incorporated a tiny piece of a species that hadn't seen Africa for a very long time.

This is really not my field, so do feel free to slap me down, but this is fascinating and it makes me wonder if there were an extant population of Homo Heidelbergensis in Europe at the same time as the Denisovans and Neanderthals. If I understand correctly, Homo Heidelbergensis were in essence Homo Erectus. Right?

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson...

I hope you aren't referring to Ötzi, the 5300 year old mummy, who most certainly does not have a living grandson.

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson. How do they know this current genome wasn't from some deformed person living 2000 years ago? They just see what they want to and report on it. Even if carbon dating places him in the "whatever"-assic period it still doesn't mean he wasn't the exception in his society. Plus, carbon dating is a flawed science in itself. Scientist still can't tell the difference from a man buried 5000 years ago and and a man buried 1000 years ago. There are so many factors at work that science does not understand yet that pertain to the fossilization and preservation of subterraneal bones buried at different depths and left untouched over the course of thousands of years. Every time they find something new buried deep they automatically assume it is 500,000 or more years old and nobody disputes them. Ice man was supposed to be an early ancestor. I remember reading the National Geographic article on it with great intrigue. Then I found out the truth and stopped trusting evolutionary scientists from that point on. Everybody was convinced Ice Man was ancient and some villager proved the entire scientific community wrong. My guess is these new skeletons are no more than 5000 years old.

You have written so much hilarity here, I felt the need to credit it.

#1. Oetzi doesn't have a grandson. He has a group of genetic descendants. Guess what? Your ancestors have a genetic descendant -- you.

#2. The DNA of this specimen in this story doesn't tell us if he was deformed. It tells us what his genetic code was. You appear to have confused phenotype (the appearance of a specimen) and genotype (the genetic code of that specimen.) But we don't know what Denisovans looked like yet because we don't have a skull or much of the skeleton.

#3. "There are so many factors at work that science does not understand yet that pertain to the fossilization and preservation of subterraneal..." Please name three factors that science does not understand well enough to accurately date these bones and derive a genome from them.

#4. " Every time they find something new buried deep they automatically assume it is 500,000 or more years old and nobody disputes them." Oetzi wasn't 500,000 years old. He is roughly 5500 years old.

You appear to have half-understood whatever it was you read and drawn ridiculous conclusions therefrom, then blamed science for your own half-assed understanding.

I found your liberal usage of the term 'human' to be inaccurate, such as:

Quote:

DNA sequencing revealed the bone to be from a Neanderthal, a different group of pre-modern humans that is most closely related to the Denisovans.

[

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

Also, i believe the species Homo Habilis had two descendant species: Homo Erectus, which migrated into Asia, and Homo Georgicus, which migrated into Europe. So, Homo Georgicus should be used in reference to this article rather than Homo Erectus.

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

That's your definition. Human could be a term applied to any organism of the genus Homo, including Homo erectus.

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

That's your definition. Human could be a term applied to any organism of the genus Homo, including Homo erectus.

The technical term being used by researchers in these publications is "archaic humans."

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson...

I hope you aren't referring to Ötzi, the 5300 year old mummy, who most certainly does not have a living grandson.

The one and the same. I remember what I read about him back when the story disappeared from the news and not what everybody claims he is now. He got trapped behind a rock during an avalanche and now he's a mummy?

When the body was first discovered, it was assumed to be a mountaineer who died within the previous few years. It wasn't until they dug it out of the ice that they realized it was much older. It was never considered a "missing link" in the evolutionary sense, being a fully modern human from only a few thousand years ago (much younger than the Neandertals and Denisovans being discussed in the article). No living grandchildren or great-grandchildren (for what are hopefully obvious reasons), but it wouldn't be surprising if some people in that area were his descendents (or at least descended from the same clan). The body and the belongings found with it have huge archaeological value, offering insights into what life was like for people in that area at that time.

The latest analysis of the remains suggests he was a victim of murder or some kind of battle; he had an arrowhead buried in his left shoulder and showed signs of head trauma, along with other peri-mortem injuries. It isn't clear whether he was killed near where he was found, or whether he was carried there from a lower altitude.

Thank you for clearing up all of my misconceptions in a kind and loving manner. I totally believe you now. How wrong was I. If you had resorted to name-calling and profanity laced retorts I would have been less likely to listen to you. You totally sold me. When my species comes to enslave this planet yours will be on the list of protected individuals.

I tend to respond in kind. You asserted that you don't trust scientists because of various reasons that have nothing to do with science and everything to do with your own misunderstanding of it. If we were talking about an esoteric point of theory or a really complicated scenario, I'd completely understand that. There's a lot of science I don't really understand, after all.

But you went on to make assertions about how a villager proved all these scientists wrong, assertions about the age of Oetzi, and assertions about the meaning of genetic variation that you could have corrected, at any point, with a simple Google search.

It's not your ignorance that's grating, but the lack of any impetus to fact check even the simplest assertions.

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson...

I hope you aren't referring to Ötzi, the 5300 year old mummy, who most certainly does not have a living grandson.

If so, he got it bass-ackwards.

That body was so well-preserved the hikers who found it thought he was victim of a recent accident or murder. Then the police started investigating, then archaeologists got involved in actually dating the remains, and proved they were a few thousand years too old for the police to be concerned with.

Grumbles "Opposable Thumbs" McGrunty is still wanted for questioning over Ötzi's suspicious death.

If any graduate students in Statistics are looking for a thesis topic, I'd like to suggest archaeology journals.

From the wikipedia article on Densiova homin.

"Analysis of genomes of modern humans show that they mated with at least two groups of ancient humans: Neanderthals (more similar to those found in the Caucasus than those from the Altai region)[7] and Denisovans.[11][12][14] Approximately 4% of the DNA of non-African modern humans is shared with Neanderthals, suggesting interbreeding.[12] Tests comparing the Denisova hominin genome with those of six modern humans – a ǃKung from South Africa, a Nigerian, a Frenchman, a Papua New Guinean, a Bougainville Islander and a Han Chinese – showed that between 4% and 6% of the genome of Melanesians (represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population. This DNA was possibly introduced during the early migration to Melanesia. These findings are in concordance with the results of other comparison tests which show a relative increase in allele sharing between the Denisovan and the Aboriginal Australian genome, compared to other Eurasians and African populations, however it has been observed that Papuans, the population of Papua New Guinea, have more allele sharing than Aboriginal Australian"

I can understand that they have limited supplies of 150,000 year old DNA, but they consider 6 people as statistically valid samples of the DNA of all modern humanity.

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson...

I hope you aren't referring to Ötzi, the 5300 year old mummy, who most certainly does not have a living grandson.

The one and the same. I remember what I read about him back when the story disappeared from the news and not what everybody claims he is now. He got trapped behind a rock during an avalanche and now he's a mummy?

When the body was first discovered, it was assumed to be a mountaineer who died within the previous few years. It wasn't until they dug it out of the ice that they realized it was much older. It was never considered a "missing link" in the evolutionary sense, being a fully modern human from only a few thousand years ago (much younger than the Neandertals and Denisovans being discussed in the article). No living grandchildren or great-grandchildren (for what are hopefully obvious reasons), but it wouldn't be surprising if some people in that area were his descendents (or at least descended from the same clan). The body and the belongings found with it have huge archaeological value, offering insights into what life was like for people in that area at that time.

The latest analysis of the remains suggests he was a victim of murder or some kind of battle; he had an arrowhead buried in his left shoulder and showed signs of head trauma, along with other peri-mortem injuries. It isn't clear whether he was killed near where he was found, or whether he was carried there from a lower altitude.

Further recent analyst of his stomach, which apparently was hard to find at first as it had migrated high up into his chest cavity, and intestines suggest (from pollen) that he had been high in the mountains, perhaps hunting or looking for copper, then came down to the lowlands, had a fairly large meal (of cooked lamb I think), before returning to the mountains, perhaps while being pursued, after being recently wounded in a vicious attack. All in all A pretty dramatic end.

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

That's your definition. Human could be a term applied to any organism of the genus Homo, including Homo erectus.

Speciation is such a fuzzy, hard to define thing anyway.

Quite a few species are regional specific variants of a broader group, and easily capable of interbreeding, should opportunity exist. Others exist in a gradient with regional epitomes with a broad range in the middle.

If you look at humans, the various subgroups are conventionally considered regional subgroups, but using some of the other classification methodology, could be different but related species altogether.

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson...

I hope you aren't referring to Ötzi, the 5300 year old mummy, who most certainly does not have a living grandson.

The OP is demonstrably stupid as well as misinformed. He's not only wrong about carbon dating, but has also managed to miscomprehend an article about Ozti's descendents living in Austria.

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

If any graduate students in Statistics are looking for a thesis topic, I'd like to suggest archaeology journals.

From the wikipedia article on Densiova homin.

"Analysis of genomes of modern humans show that they mated with at least two groups of ancient humans: Neanderthals (more similar to those found in the Caucasus than those from the Altai region)[7] and Denisovans.[11][12][14] Approximately 4% of the DNA of non-African modern humans is shared with Neanderthals, suggesting interbreeding.[12] Tests comparing the Denisova hominin genome with those of six modern humans – a ǃKung from South Africa, a Nigerian, a Frenchman, a Papua New Guinean, a Bougainville Islander and a Han Chinese – showed that between 4% and 6% of the genome of Melanesians (represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population. This DNA was possibly introduced during the early migration to Melanesia. These findings are in concordance with the results of other comparison tests which show a relative increase in allele sharing between the Denisovan and the Aboriginal Australian genome, compared to other Eurasians and African populations, however it has been observed that Papuans, the population of Papua New Guinea, have more allele sharing than Aboriginal Australian"

I can understand that they have limited supplies of 150,000 year old DNA, but they consider 6 people as statistically valid samples of the DNA of all modern humanity.

I'm pretty sure that each field has its own standards of what reaches significance since they all have different levels of data to work with; not everyone can get enough data to go six-sigma like they do at CERN. It could also very well be that the selection and modeling of just those six modern samples were informed by many other studies of hundreds of other samples; sequencing is long and expensive so you can't always do hundreds every time you need to do a comparison with a single sample. A lay person comes to the article and sees "oh they just compared with six samples" but someone versed in the field sees those six samples plus all of the previous work that's gone into other studies and other samples like that.

Edit: It also bears noting that those six samples could have come from populations with very little breeding outside of their groups (the !Kang and Bougainville Islander at the very least), in which case, yes, they would be very representative of their population.

Yeah, the fact that anyone is suprised that we interbred with Neanderthals at some point shocks me. People "lay" with farm animals, why not something that looks mostly like us? I mean, heck, furrys and plushies are a thing!

It doesn't take much more than someone to have an uncle cletus in their caveman tribe to get some of those genes going.